Hi, Wouldn't it be better to use a program written especially for this purpose, like dang/dangle from the richardson group, or dssp (, or others I don't know of)?
Of course, you may have a specific reason for using pymol, so this is just a suggestion! gilleain torrance On Wed, Jun 11, 2008 at 2:20 PM, David McGiven <david.mcgi...@fusemail.com> wrote: > > Dear PyMol Users, > > We're using Pymol to automatically extract all the backbone dihedrals > from a protein. > > I've noticed that it's very slow doing those calculations. Normally in > Fortran it will take some seconds, while in pymol it takes five minutes > or even more. > > The command we issue is : > > $> /opt/soft/pymol/pymol -qc dihedral.py > > That dihedral.py script only reads some pdb's and and uses the function > get_dihedral() > > Does anybody know why is it running so slow ? And if so, is it possible > to speed it up in any way ? > > Thanks > > Best Regards, > David McGiven. > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
